What if you could rerun computational experiments from within a scientific paper?
The GenePattern add-on for Word for Windows integrates reusable genomic experiment pipelines into Microsoft Word. Readers can rerun the original or modified experiments from within the document by connecting to a GenePattern server.
Rerunning a pipeline inside Word
I don’t run Windows, so I took this screenshot from a video produced at the Broad Institute of MIT and Harvard, where GenePattern is developed.
Readers without Word for Windows can also access the experimental pipelines by exporting them from the document: just run a GenePatternDocumentExtractor command from a GenePattern server. The GenePattern public server was very easy to access and start using. Here’s what the GenePatternDocumentExtractor command looks like:
Running GenePatternDocumentExtractor at the GenePattern public server
Unfortunately the jobs I ran didn’t extract any pipelines from the Institute’s sample DOC. I’ve sent in an inquiry (either I’m doing something wrong or there’s a bug, either way it’s useful). I was very impressed that I could make my jobs public, then refer to them by URL in my email, to make clear what exactly I did.
The GenePattern add-on for Word is another find from the beyondthepdf list. Its development was funded by Microsoft. See also Accessible Reproducible Research by Jill P. Mesirov (Science, 327:415, 2010). doi:10.1126/science.1179653, which describes the underlying philosophy: have a Reproducible Research System (RRS) made up of an environment for doing computational work (the Reproducible Research Environment or RRE) and an authoring environment (the Reproducible Research Publisher or RRP) which links back to the research system.
Tags: beyondthePDF, GenePattern, Microsoft Word, Reproducible Research Environment, Reproducible Research Publisher, Reproducible Research System, Word for Windows
Posted in books and reading, future of publishing, information ecosystem, scholarly communication, Uncategorized | Comments (1)
Tim van Gelder provides a taxonomy for decisions:
- Intuitive Decisions
- Technical Decisions
- Deliberative Decisions
- Bureaucratic Decisions
Deliberative and bureaucratic decisions are, I think, the most important for collaborative decision-making. Intuitive decisions, made quickly by an individual, are least important for collaboration. Technical decisions have the most interesting description: they are “made by following some well-defined technical procedure”; arguably they are not decisions.
Can you spot any overlaps or gaps? Discuss at his article.
The argumentation community has given a lot of attention to deliberation; I wonder if that has been influenced by the prevalence of deliberation in decision-making, and the difficulty of formal modelling of bureaucracies.
Tags: decision-making, taxonomies
Posted in argumentative discussions, PhD diary | Comments (0)
I wrote Springer to ask about buying an ebook that’s not in our university subscriptions. They sell the print copy at €62.95, but the electronic copy comes to €425, chapter by chapter.
Publishers: this is short-sighted (not to mention frustrating)–especially when your customers are looking for a portable copy of a book they already owns!
———- Forwarded message ———-
From: Springerlink, Support, Springer DE
Date: Fri, Oct 29, 2010 at 8:46 PM
Subject: WG: ebook pricing
Thank you for your message.
On SpringerLink you can purchase online single journal articles and book chapters, but no complete ebooks.
eBooks are sold by Springer in topical eBook packages only.
with kind regards,
SpringerLink Support Team
eProduct Management & Innovation | SpringerLink Operations
email@example.com | + 49 (06221) 4878 743
From: Jodi Schneider
Sent: Thursday, October 28, 2010 5:09 PM
To: MetaPress Support
Subject: ebook pricing
I’m interested in buying a copy of [redacted] as an ebook:
This book has 17 chapters, which seem to be priced at 25 EUR each = 425 EUR.
But I could buy a print version, new at springer.com for 62.95 EUR:
Can you help me get the ebook at this price?
Tags: business models, ebooks, format agnosticism, price gouging, Springer
Posted in books and reading, future of publishing | Comments (3)